Complex Formation in Aqueous Trimethylamine-N-oxide (TMAO) Solutions

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes

Trimethylamine N-oxide (TMAO) as a representative natural osmolyte has received much attention because of its unique properties, including enhancement of hydrogen bonding networks in liquid water and stabilization of three-dimensional structures of proteins in living organisms. As a hydrogen bond maker and/or a protein stabilizer, its hydrated structures and orientation dynamics in aqueous solutions have been investigated by various spectroscopic methods. Particularly, distinct from other natural osmolytes, it has been found that TMAO molecules form complexes with water molecules even at low concentrations, showing extraordinarily long lifetimes and much larger effective dipole moments. In this study, we demonstrated that collective motions of water molecules are closely correlated to TMAO molecules, as revealed by the changes of the librational modes observed in hyper-Raman (HR) spectra in the low-frequency region (<1000 cm-1) for the first time. Based on HR spectra of the TMAO solutions at submolar concentrations, we observed that the librational bands originating from water apparently upshift (∼15 cm-1) upon the addition of TMAO molecules. Compared to the OH stretching band of water showing a negligible downshift (<5 cm-1), the librational bands of water are more sensitive to reflect changes in the hydrogen bonding networks in the TMAO solutions, suggesting formation of transient TMAO-water complexes plays an essential role toward surrounding water molecules in perturbing their librational motions. We expect to provide a supplementary approach to understand that water molecules in TMAO aqueous solutions are strongly affected by TMAO molecules, different from other osmolytes.

Effect of trimethylamine-N-oxide on the phase separation of aqueous polyethylene glycol-600-Dextran-75 two-phase systems

The emergence of phase separation in both intracellular biomolecular condensates (membrane-less organelles) and in vitro aqueous two-phase systems (ATPS) relies on the formation of immiscible water-based phases/domains. The solvent properties and arrangement of hydrogen bonds within these domains have been shown to differ and can be modulated with the addition of various inorganic salts and osmolytes. The naturally occuring osmolyte, trimethylamine-N-oxide (TMAO), is well established as a biological condensate stabilizer whose presence results in enhanced phase separation of intracellular membrane-less compartments. Here, we show the unique effect of TMAO on the mechanism of phase separation in model PEG-600-Dextran-75 ATPS using dynamic and static light scattering in conjunction with ATR-FTIR and solvatochromic analysis. We observe that the presence of TMAO may enhance or destabilize phase separation depending on the concentration of phase forming components. Additionally, the behavior and density of mesoscopic polymer agglomerates, which arise prior to macroscopic phase separation, are altered by the presence and concentration of TMAO.

What is behind a gas stream scrubbing liquid? Monoethanolamine/water mixtures as seen by dielectric relaxation spectroscopy

High-quality dielectric data for monoethanolamine (MEA)/water mixtures covering the entire miscibility range are presented. For MEA concentrations c1 ≥ 1 M the obtained complex permittivity spectra, covering the frequency range from 0.05 to 89 GHz, are best described by a sum of four Debye relaxations. Modes at ∼3 GHz and ∼10 GHz are solute-specific. Whilst the first can be assigned to MEA aggregates, the second is a composite arising from "free" MEA dipoles with dynamically retarded water hydrating them. The relaxations at ∼18 GHz and ∼200 GHz essentially reflect the cooperative H-bond fluctuations of more-or-less unperturbed "bulk" water, albeit with minor solute contributions. Evaluation of the bulk-water amplitude reveals that in water-rich mixtures (c1 ≤ 3.5 M) Zt = 3.5 ± 0.2 H2O molecules hydrate a MEA molecule. Then Zt drops linearly, reaching zero for neat MEA. Supported by the literature, this concentration dependence suggests that only H2O molecules H-bonded to the NH2 and OH groups of MEA contribute to Zt. At concentrations beyond hydration shell overlap (c1 ≥ 3.5 M) these H-bonds are gradually eliminated, while new interactions with neighboring MEA molecules are formed. From the evaluation of the MEA-specific amplitudes we conclude that for c1 ≥ 2 M, including neat MEA, ∼35% of the solute molecules are in aggregates, where breaking the intermolecular NH⋯O hydrogen bond determines the dynamics.

Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor

The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.

TMAO: Protecting proteins from feeling the heat

Osmolytes are ubiquitous in the cell and play an important role in controlling protein stability under stress. The natural osmolyte trimethylamine N-oxide (TMAO) is used by marine animals to counteract the effect of pressure denaturation at large depths. The molecular mechanism of TMAO stabilization against pressure and urea denaturation has been extensively studied, but unlike the case of other osmolytes, the ability of TMAO to protect proteins from high temperature has not been quantified. To reveal the effect of TMAO on folded and unfolded protein ensembles and the hydration shell at different temperatures, we study a mutant of the well-characterized, fast-folding model protein B (PRB). We carried out, in total, >190 μs all-atom simulations of thermal folding/unfolding of PRB at multiple temperatures and concentrations of TMAO. The simulations show increased thermal stability of PRB in the presence of TMAO. Partly structured, compact ensembles are favored over the unfolded state. TMAO forms two shells near the protein: an outer shell away from the protein surface has altered H-bond lifetimes of water molecules and increases hydration of the protein to help stabilize it; a less-populated inner shell with an opposite TMAO orientation closer to the protein surface binds exclusively to basic side chains. The cooperative cosolute effect of the inner and outer shell TMAO has a small number of TMAO molecules "herding" water molecules into two hydration shells at or near the protein surface. The stabilizing effect of TMAO on our protein saturates at 1 M despite higher TMAO solubility, so there may be little evolutionary pressure for extremophiles to produce higher intracellular TMAO concentrations, if true in general.

Theoretical Spectroscopy Aided Validation of the Hydration Structure of Trimethylamine N-Oxide (TMAO)

The molecular-level understanding of the hydration structure of external solutes is extremely challenging. In the context of molecular simulation, particularly sampling proper solvation structure by classical force fields remains always a matter of concern. In the present work, we use theoretical vibrational spectroscopy to understand the microscopic solvation structure of TMAO in water in the cases of five different classical force fields of TMAO. We find that the Netz (J. Phys. Chem. B 2013, 117, 8310-8321) force field agrees better with the experimental results. We also observe that the O-H stretching frequency gets red-shifted compared to the bulk water response, suggesting that the TMAO-water forms stronger hydrogen bonds than water-water. We further investigate the O-H stretching frequency in different solvation shells and the hydrophobic and hydrophilic regions of TMAO. We find that, in the hydrophilic region, O-H stretching frequencies show a strong orientational correlation; however, that is absent in the hydrophobic region. These are further supplemented by hydrogen-bond analysis and local structure index data.

TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions

Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in cells in response to osmotic stress. TMAO stabilizes proteins by the entropic stabilization mechanism, which pictures TMAO as a nanocrowder that predominantly destabilizes the unfolded state. However, the mechanism of action of TMAO on RNA is much less understood. Here, we use all-atom molecular dynamics simulations to investigate how TMAO interacts with a 12-nt RNA hairpin with a high melting temperature, and an 8-nt RNA hairpin, which has a relatively fluid native basin in the absence of TMAO. The use of the two hairpins with different free energy of stabilization allows us to probe the origin of the destabilization effect of TMAO on RNA molecules without the possibility of forming tertiary interactions. We generated multiple trajectories using all-atom molecular dynamics (MD) simulations in explicit water by employing AMBER and CHARMM force fields, both in the absence and presence of TMAO. We observed qualitatively similar RNA-TMAO interaction profiles from the simulations using the two force fields. TMAO hydrogen bond interactions are largely depleted around the paired RNA bases and ribose sugars. In contrast, we show that the oxygen atom in TMAO, the hydrogen bond acceptor, preferentially interacts with the hydrogen bond donors in the solvent exposed bases, such as those in the stem-loop and the destabilized base stacks in the unfolded state, especially in the marginally stable 8-nt RNA hairpin. The predicted destabilization mechanism through TMAO-RNA hydrogen bond interactions could be tested using two-dimensional IR spectroscopy. Since TMAO does not significantly interact with the hydroxyl group of the ribose sugars, we predict that similar results must also hold for DNA.

Typical at glance but interesting when analyzed in detail: A story of Tris hydration

This paper provides results of dielectric relaxation (DR) spectroscopy of aqueous solutions of tris(hydroxymethyl)aminomethane (Tris) covering frequencies of 0.05 ≤ ν/GHz ≤89. The DR spectra can be well fit by a sum of Cole-Cole relaxation, assigned to the solute, and 2 Debye modes already observed for neat water. Analysis of the amplitudes reveals that Tris is hydrated by 7 H₂Os up to its solubility limit. However, the rather high effective solute dipole moment of ≈12 D suggests that H₂O dipoles in contact with Tris should reorient independently from it. Accordingly, an alternative description of the DR spectra with a superposition of 4 Debyerelaxations was attempted. In this model, the slowest mode at ∼4 GHz arises from solute reorientation and that at ∼8 GHz was assigned to dynamically retarded hydration water, whereas relaxations at ∼18 and ∼500 GHz are again those of (rather unperturbed) bulk water. Analysis of the solvent-related modes shows that Tris indeed slows down 7-8 H₂O molecules. However, the solute-solvent interaction strength is rather weak, excluding the rotation of an alleged Tris-(7-8) H₂O cluster as an entity. The now derived effective dipole moment of (6.3 ± 0.5) D for the bare Tris molecule allows speculations on its conformation. With the help of computational methods, we suggest that Tris dissolved in water most likely possesses an intramolecular H-bond between the nitrogen and hydrogen atoms of amino and hydroxyl groups, respectively. In addition, computational results indicate that the seven hydration H₂Os found by DR bind directly to the Tris OH groups.

Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems

The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.

Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water

Although small organic molecules in cells have been considered important to control the functions of proteins, their electronic fluctuation and the intermolecular interaction, which is physicochemical origin of the molecular functions, under physiological conditions, i.e., dilute aqueous solutions (0.18 mol L^-1), has never been clarified due to the lack of observation methods with both accuracy and efficiency. Herein, the time evolutions of the interactions in dilute aqueous trimethylamine N-oxide (TMAO) and tert-butyl alcohol (TBA) solutions were analyzed via ab initio molecular dynamics simulations accelerated with the fragment molecular theory. It has been known that TMAO and TBA have similar structures, but opposite physiological functions to stabilize and destabilize proteins. It was clarified that TMAO induced stable polarization and charge-transfer interactions with water molecules near the hydrophilic group, and water molecules were caught even near the CH₃- group. Those should affect protein stabilization. Understanding the solution dynamics will contribute to artificial chaperone design in next generation medicine.

Elucidating Conformation and Hydrogen-Bonding Motifs of Reactive Thiourea Intermediates

Substituted diphenylthioureas (DPTUs) are efficient hydrogen-bonding organo-catalysts, and substitution of DPTUs has been shown to greatly affect catalytic activity. Yet, both the conformation of DPTUs in solution and the conformation and hydrogen-bonded motifs within catalytically active intermediates, pertinent to their mode of activation, have remained elusive. By combining linear and ultrafast vibrational spectroscopy with spectroscopic simulations and calculations, we show that different conformational states of thioureas give rise to distinctively different N–H stretching bands in the infrared spectra. In the absence of hydrogen-bond-accepting substrates, we show that vibrational structure and dynamics are highly sensitive to the substitution of DPTUs with CF₃ groups and to the interaction with the solvent environment, allowing for disentangling the different conformational states. In contrast to bare diphenylthiourea (0CF-DPTU), we find the catalytically superior CF₃-substituted DPTU (4CF-DPTU) to favor the trans–trans conformation in solution, allowing for donating two hydrogen bonds to the reactive substrate. In the presence of a prototypical substrate, DPTUs in trans–trans conformation hydrogen bond to the substrate’s C=O group, as evidenced by a red-shift of the N–H vibration. Yet, our time-resolved infrared experiments indicate that only one N–H group forms a strong hydrogen bond to the carbonyl moiety, while thiourea’s second N–H group only weakly interacts with the substrate. Our data indicate that hydrogen-bond exchange between these N–H groups occurs on the timescale of a few picoseconds for 0CF-DPTU and is significantly accelerated upon CF₃ substitution. Our results highlight the subtle interplay between conformational equilibria, bonding states, and bonding lifetimes in reactive intermediates in thiourea catalysis, which help rationalize their catalytic activity.

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions

We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine N-oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.

Analytical modeling of micelle growth. 5. Molecular thermodynamics of micelles from zwitterionic surfactants

HYPOTHESIS

The critical micelle concentration, aggregation number, shape and length of spherocylindrical micelles in solutions of zwitterionic surfactants can be predicted by knowing the molecular parameters and surfactant concentrations. This can be achieved by upgrading the quantitative molecular thermodynamic model with expressions for the electrostatic interaction energy between the zwitterionic dipoles and micellar hydrophobic cores of spherical and cylindrical shapes.

THEORY

The correct prediction of the mean micellar aggregation numbers requires precise calculations of the free energy per molecule in the micelles. New analytical expressions for the dipole electrostatic interaction energy are derived based on the exact solutions of the electrostatic problem for a single charge close to a boundary of spherical and cylindrical dielectric media. The obtained general theory is valid for arbitrary ratios between dielectric constants, radii of spheres and cylinders, positions, and orientations of dipoles.

FINDINGS

The detailed numerical results show quantitatively the effects of the micelle curvature and dielectric properties of the continuum media on the decrease of the dipole electrostatic interaction energy. Excellent agreement was achieved between the theoretical predictions and experimental data for the critical micelle concentration, size and aggregation number of zwitterionic surfactant micelles. This study can be extended to mixed micelles of zwitterionic and ionic surfactants in the presence of salt to interpret and predict the synergistic effect on the rheology of solutions.

Temperature induced change of TMAO effects on hydrophobic hydration

The effect of trimethylamine-N-oxide (TMAO) on hydrophobic solvation and hydrophobic interactions of methane has been studied with Molecular Dynamics simulations in the temperature range between 280 and 370 K at 1 bar ambient pressure. We observe a temperature transition in the effect of TMAO on the aqueous solubility of methane. At low temperature (280 K), methane is preferentially hydrated, causing TMAO to reduce its solubility in water, while above 320 K, methane preferentially interacts with TMAO, causing TMAO to promote its solubility in water. Based on a statistical-mechanical analysis of the excess chemical potential of methane, we find that the reversible work of creating a repulsive methane cavity opposes the solubility of methane in TMAO/water solution more than in pure water. Below 320 K, this solvent-excluded volume effect overcompensates the contribution of methane–TMAO van der Waals interactions, which promote the solvation of methane and are observed at all temperatures. These van der Waals interactions with the methyl groups of TMAO tip the balance above 320 K where the effect of TMAO on solvent-excluded volume is smaller. We furthermore find that the effective attraction between dissolved methane solutes increases with the increasing TMAO concentration. This observation correlates with a reduction in the methane solubility below 320 K but with an increase in methane solubility at higher temperatures.

In silico all-atom approach to thermodiffusion in dilute aqueous solutions

Thermodiffusion (or thermophoresis) is the phenomenon by which the spatial distributions of constituents of liquid or gas phases become inhomogeneous in response to a temperature gradient. It has been evidenced in a variety of systems and has many practical applications as well as implications in the context of the origins of life. A complete molecular picture of thermophoresis is still missing, and phenomenological approaches are often employed to account for the experimental observations. In particular, the amplitude of the resulting concentration-gradients (quantified by the Soret coefficient) depends on many factors that are not straightforwardly rationalized. All-atom molecular dynamics simulations appear as an exquisite tool to shed light on the molecular origins for this phenomenon in molecular systems, but the practical implementation of thermophoretic settings in silico poses significant challenges. Here, we propose a robust approach to tackle thermophoresis in dilute realistic solutions at the molecular level. We rely on a recent enhanced heat-exchange algorithm to generate temperature-gradients. We carefully assess the convergence of thermophoretic simulations in dilute aqueous solutions. We show that simulations typically need to be propagated on long timescales (hundreds of nanoseconds). We find that the magnitude of the temperature gradient and the box sizes have little effect on the measured Soret coefficients. Practical guidelines are derived from such observations. Provided with this reliable setup, we discuss the results of thermophoretic simulations on several examples of molecular, neutral solutes, which we find in very good agreement with experimental measurements regarding the concentration-, mass-, and temperature-dependence of the Soret coefficient.

Interaction of Zwitterionic Osmolyte Trimethylamine N-oxide (TMAO) with Molecular Hydrophobes: An Interplay of Hydrophobic and Electrostatic Interactions

Interaction of trimethylamine N-oxide (TMAO) with charged/uncharged moieties of proteins and lipids is an important elementary step toward the multifaceted biofunctions of TMAO. Using minimum area Raman difference spectroscopy (MA-RDS) of aqueous TMAO (1.0 M) in the presence of deuterated molecular hydrophobes (e.g., deuterated tetramethylammonium cation (d-TMA⁺) and tert-butylalcohol (d-TBA)), we show that TMAO exhibits two distinct motifs of interaction with the cationic (d-TMA⁺) and uncharged (d-TBA) hydrophobes. Specifically, the trimethylammonium moiety of TMAO undergoes van der Waals attraction with the tert-butyl group of d-TBA, which is governed by their mutual hydrophobic interaction with water. This makes their methyl groups less exposed to water. In contrast, for the cationic hydrophobe (d-TMA⁺), TMAO interacts electrostatically via its negatively charged-oxygen, which in turn orients the TMAO-methyls away from the hydrophobe (d-TMA⁺), keeping them exposed to water.

Aqueous TMAO solution under high hydrostatic pressure

Trimethylamine N-oxide (TMAO) is a well known osmolyte in nature, which is used by deep sea fish to stabilize proteins against High Hydrostatic Pressure (HHP). We present a combined ab initio molecular dynamics, force field molecular dynamics, and THz absorption study of TMAO in water up to 12 kbar to decipher its solvation properties upon extreme compression. On the hydrophilic oxygen side of TMAO, AIMD simulations at 1 bar and 10 kbar predict a change of the coordination number from a dominating TMAO·(H₂O)₃ complex at ambient conditions towards an increased population of a TMAO·(H₂O)₄ complex at HHP conditions. This increase of the TMAO-oxygen coordination number goes in line with a weakening of the local hydrogen bond network, spectroscopic shifts and intensity changes of the corresponding intermolecular THz bands. Using a pressure-dependent HHP force field, FFMD simulations predict a significant increase of hydrophobic hydration from 1 bar up to 4-5 kbar, which levels off at higher pressures up to 10 kbar. THz spectroscopic data reveal two important pressure regimes with spectroscopic inflection points of the dominant intermolecular modes: The first regime (1.5-2 kbar) is barely recognizable in the simulation data. However, it relates well with the observation that the apparent molar volume of solvated TMAO is nearly constant in the biologically relevant pressure range up to 1 kbar as found in the deepest habitats on Earth in the ocean. The second inflection point around 4-5 kbar is related to the amount of hydrophobic hydration as predicted by the FFMD simulations. In particular, the blueshift of the intramolecular CNC bending mode of TMAO at about 390 cm^-1 is the spectroscopic signature of increasingly pronounced pressure-induced changes in the solvation shell of TMAO. Thus, the CNC bend can serve as local pressure sensor in the multi-kbar pressure regime.

Microscopic structural features of water in aqueous-reline mixtures of varying compositions

Reline, a mixture of urea and choline chloride in a 2 : 1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cations can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We carry out extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on the microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between 26.3 and 91.4 wt%. A disruption of the local hydrogen-bonded structure in water is observed upon inclusion of urea and choline chloride. The extent of deviation of the water structure from tetrahedrality is quantified using the tetrahedral order parameter (q_tet). Our analyses show a monotonic increase in the structural disorder as the co-solvents are added. Increase in the q_tet values are observed when highly electro-negative hetero-atoms like nitrogen, oxygen of urea and choline cations are counted as partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network in water and we observe the gradual rupturing of water-water hydrogen bonds and their subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cations has also been found. Considering all the constituents as the hydrogen bond partners we calculate the possibility of a successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

Hydration and dynamics of L-glutamate ion in aqueous solution

Aqueous solutions of sodium l-glutamate (NaGlu) in the concentration range 0 < c/M ≤ 1.90 at 25 °C were investigated by dielectric relaxation spectroscopy (DRS) and statistical mechanics (1D-RISM and 3D-RISM calculations) to study the hydration and dynamics of the l-glutamate (Glu-) anion. Although at c → 0 water molecules beyond the first hydration shell are dynamically affected, Glu- hydration is rather fragile and for c ⪆ 0.3 M apparently restricted to H2O molecules hydrogen bonding to the carboxylate groups. These hydrating dipoles are roughly parallel to the anion moment, leading to a significantly enhanced effective dipole moment of Glu-. However, l-glutamate dynamics is determined by the rotational diffusion of individual anions under hydrodynamic slip boundary conditions. Thus, the lifetime of the hydrate complexes, as well as of possibly formed [Na+Glu-]0 ionpairs and l-glutamate aggregates, cannot exceed the characteristic timescale for Glu- rotation.

Confined Water Molecules in Binary Mixtures of Water and 2,6-Lutidine Near Lower Solution Critical Temperature

We study the concentration and temperature dependence of the reorientation dynamics of water molecules in binary mixtures of water and 2,6-lutidine below the lower solution critical temperature (LSCT) with femtosecond mid-infrared pump–probe spectroscopy. The measurements reveal the presence of water molecules interacting with both the hydrophobic groups of lutidine and forming a hydrogen bond with the nitrogen atom of lutidine. Both types of molecules show a strongly decreased rotational mobility in comparison to bulk water. From the temperature dependence of the slow water fraction, we conclude that the lutidine molecules form clusters that decrease in size when the temperature is decreased further below the LSCT.

Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes

The molecular mechanism of osmolytes on the stabilization of native states of protein is still controversial irrespective of extensive studies over several decades. Recent investigations in terms of experiments and molecular dynamics simulations challenge the popular osmophobic model explaining the mechanistic action of protein-stabilizing osmolytes. The current Perspective presents an updated view on the mechanistic action of osmolytes in light of resurgence of interesting experiments and computer simulations over the past few years in this direction. In this regard, the Perspective adopts a bottom-up approach starting from hydrophobic interactions and eventually adds complexity in the system, going toward the protein, in a complex topology of hydrophobic and electrostatic interactions. Finally, the Perspective unifies osmolyte-induced protein conformational equilibria in terms of preferential interaction theory, irrespective of individual preferential binding or exclusion of osmolytes depending on different osmolytes and protein surfaces. The Perspective also identifies future research directions that can potentially shape this interesting area.

Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine-N-oxide on the Peptide Solvation Shell

The osmolyte trimethylamine-N-oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA, 2017, 114, 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.

Mitigating effects of osmolytes on the interactions between nanoparticles and supported lipid bilayer

To maintain osmotic balance, cells usually produce neutral solutes (i.e., osmolytes), together with charged species to cope with salinity stress. Osmolytes are known to be important in stabilizing/destabilizing macromolecules (e.g., proteins) via depletion /accumulation around their surfaces. To better understand the physiological fate of nanoparticles (NPs), we investigated the effect of osmolytes [(urea and trimethylamine N-oxide (TMAO)] and specific anions (NO₃^- and F^-) on the interactions between NPs and supported lipid bilayers (SLBs). Carboxylated polystyrene NPs (60 nm) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were chosen as model NPs and lipid. Quartz crystal microbalance with dissipation monitoring (QCM-D) was used to quantify NP deposition dynamics. Microscale thermophoresis (MST) was used to characterize the affinity between DOPC vesicles (or NPs) and osmolytes. Our results show that osmolytes are capable of protecting SLBs from NP-induced disruption. Upon NP deposition onto supported vesicle layers (SVLs), the leakage of encapsulated dyes decreased with the addition of osmolytes. The combination of kosmotropes (TMAO and F^-) are more efficient than that of chaotropes (urea and NO₃^-) in weakening the hydrophobic interaction between NPs and SLBs by preferential binding to NPs and/or SLBs.

Dynamical Model for the Counteracting Effects of Trimethylamine N-Oxide on Urea in Aqueous Solutions under Pressure

Of cosolutes found in living cells, urea denatures and trimethylamine N-oxide (TMAO) stabilizes proteins; furthermore, these effects cancel at a 2:1 ratio of urea to TMAO. Interestingly, cartilaginous fish use urea and TMAO as osmolytes at similar ratios at the ocean surface but with increasing fractions of TMAO at increasing depths. Here, molecular dynamics simulations of aqueous solutions with different urea:TMAO ratios show that the diffusion coefficients of water in the solutions vary with pressure if the urea:TMAO ratio is constant, but strikingly, they are almost pressure independent at the ratio found in these fish as a function of depth. This suggests that this ratio may be maintaining a homeostasis of water dynamics. In addition, diffusion is determined by hydrogen-bond lifetimes of the different species in the solution. Based on these observations, a dynamical model in terms of hydrogen-bond lifetimes is developed for the hydrogen bonding propensities of cosolutes and water in an aqueous solution to proteins. This model provides an explanation for both the counteracting effects of TMAO on urea denaturation and the depth-dependent urea:TMAO ratio found in cartilaginous fish.

Hydration in aqueous osmolyte solutions: the case of TMAO and urea

X-ray Raman scattering spectroscopy and first principles simulations reveal details of the hydration and hydrogen-bond topology of trimethylamine N-oxide (TMAO) and urea in aqueous solutions.

Vibrational mode frequency correction of liquid water in density functional theory molecular dynamics simulations with van der Waals correction

We develop a frequency correction scheme for the stretch and bending modes of liquid water, which substantially improves the prediction of the vibrational spectra.

Hydrophobic pattern of alkylated ureas markedly affects water rotation and hydrogen bond dynamics in aqueous solution

Alkylated ureas are frequently used amphiphiles to mediate biomolecule water interactions, yet their hydrophobic substitution pattern critically affects their function. These differences can be traced back to their hydration, which is poorly understood. Here, we investigate subtle effects of the hydrophobic pattern of ureas on hydration dynamics using a combination of linear and non-linear infrared spectroscopies on the OD stretching vibration of HDO. Isomeric 1,3-dimethylurea (1,3-DMU), 1,1-dimethylurea (1,1-DMU) and 1-ethylurea (1-EU) exhibit very similar and rather weak modulation of the water hydrogen-bond strength distribution. Yet, only 1,3-DMU and 1,1-DMU enhance the hydrogen-bond heterogeneity and slow-down its fluctuation dynamics. In turn, rotational dynamics of water molecules, which is dominated by hydrogen bond switches, is significantly impeded in the presence of 1,3-DMU and only weakly by 1,1-DMU and 1-EU. These marked differences can be explained by both excluded volume effects in hydration and self-aggregation, which may be the key to their biotechnological function.

Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior?

Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.

Dynamics of Dicyanamide in Ionic Liquids is Dominated by Local Interactions

The dynamics of probe molecules is commonly used to investigate the structural dynamics of room-temperature ionic liquids; however, the extent to which this dynamics reflects the dynamics of the ionic liquids or is probe specific has remained debated. Here, we explore to what extent the vibrational and rotational dynamics of the dicyanamide anion, a common ionic liquid anion, correlates with the structural relaxation of ionic liquids. We use polarization-resolved, ultrafast infrared spectroscopy to probe the temperature- and probe-concentration-dependent dynamics of samples with small amounts of 1-ethyl-3-methylimidazolium ([emim]⁺) dicyanamide ([DCA]⁻) dissolved in four [emim]⁺-based ionic liquids with tetrafluoroborate ([BF₄]⁻), bis(trifluoromethylsulfonyl)imide ([NTf₂]⁻), ethylsufate ([EtSO₄]⁻), and triflate ([OTf]⁻) as anions. The transient spectra after broad-band excitation at 2000–2300 cm^–1, resonant with the symmetric and antisymmetric C≡N stretching vibrations, initially contain oscillatory signatures due to the vibrational coherence between both modes. Vibrational population relaxation occurs on two distinct time scales, ∼6–7 and ∼15–20 ps. The vibrational dynamics is rather insensitive to the details of the ionic liquid anion and temperature, except for the slow vibrational relaxation component. The decay of the excitation anisotropy, a measure of the rotational dynamics of [DCA]⁻, markedly depends on temperature, and the obtained decay time exhibits an activation energy of ∼15–21 kJ/mol. Remarkably, neither the rotation time nor the activation energy can be simply explained by the variation of the macroscopic viscosity. Hence, our results suggest that the dynamics of dicyanamide is only in part representative of the ionic liquid structural dynamics. Rather, the dynamics of the probe anion seems to be determined by the specific interaction of [DCA]⁻ with the ionic liquid’s ions for the class of [emim]⁺-based ionic liquids studied here.

Dynamical Effects of Trimethylamine N-Oxide on Aqueous Solutions of Urea

Trimethylamine N-oxide (TMAO) stabilizes protein structures, whereas urea destabilizes proteins, and their opposing effects can be counteracted at a 1:2 ratio of TMAO to urea. To investigate how they affect solution dynamics, molecular dynamics simulations have been carried out for aqueous solutions of TMAO and urea at different concentrations. In the binary solutions, urea mainly slows the diffusion of waters that are hydrogen bonded to it (i.e., hydration water), whereas TMAO dramatically slows the diffusion of both hydration water and bulk water because of long-lived TMAO-water hydrogen bonds. In the ternary solutions, because TMAO decreases the diffusion rate of bulk water, the lifetimes of not only water-water but also urea-water hydrogen bonds increase. In addition, the constant forming and breaking of short lifetime hydrogen bonds between urea and water appears to impart energy into the bulk, whereas the long lifetime hydrogen bonds between TMAO and water slows down the bulk, resulting in the compensating effects on bulk water in the ternary solution. This suggests that the counteracting effects of TMAO on urea denaturation may be both to make longer lived hydrogen bonds to water and to counter the energizing effects of urea on bulk water.

Phonon Spectrometric Evaluation of the Solute-Solvent Interface in Solutions of Glycine and Its N-Methylated Derivatives

From the perspective of O:H-O bond cooperativity, we analyzed the solute capability of transiting the O:H-O bond from the mode of ordinary water to the hydration state and its consequence on the solution viscosity and surface stress. Phonon spectrometric results suggest that glycine and its N-methyl derivatives strongly affect the surrounding solvent molecules through H ↔ H repulsion and dipolar polarization. The H ↔ H interproton repulsion disrupts the surface stress, and the polarization enhances the solution viscosity.

Water-Mediated Protein-Protein Interactions at High Pressures are Controlled by a Deep-Sea Osmolyte

The influence of natural cosolvent mixtures on the pressure-dependent structure and protein-protein interaction potential of dense protein solutions is studied and analyzed using small-angle X-ray scattering in combination with a liquid-state theoretical approach. The deep-sea osmolyte trimethylamine-N-oxide is shown to play a crucial and singular role in its ability to not only guarantee sustainability of the native protein's folded state under harsh environmental conditions, but it also controls water-mediated intermolecular interactions at high pressure, thereby preventing contact formation and hence aggregation of proteins.

Cosolvent Effects on Polymer Hydration Drive Hydrophobic Collapse

Water-mediated hydrophobic interactions play an important role in self-assembly processes, aqueous polymer solubility, and protein folding, to name a few. Cosolvents affect these interactions; however, the implications for hydrophobic polymer collapse and protein folding equilibria are not well-understood. This study examines cosolvent effects on the hydrophobic collapse equilibrium of a generic 32-mer hydrophobic polymer in urea, trimethylamine- N-oxide (TMAO), and acetone aqueous solutions using molecular dynamics simulations. Our results unveil a remarkable cosolvent-concentration-dependent behavior. Urea, TMAO, and acetone all shift the equilibrium toward collapsed structures below 2 M cosolvent concentration and, in turn, to unfolded structures at higher cosolvent concentrations, irrespective of the differences in cosolvent chemistry and the nature of cosolvent-water interactions. We find that weakly attractive polymer-water van der Waals interactions oppose polymer collapse in pure water, corroborating related observations reviewed by Ben-Amotz ( Annu. Rev. Phys. Chem. 2016, 67, 617-638). The cosolvents studied in the present work adsorb at the polymer/water interface and expel water molecules into the bulk, thereby effectively removing the dehydration energy penalty that opposes polymer collapse in pure water. At low cosolvent concentrations, this leads to cosolvent-induced stabilization of collapsed polymer structures. Only at sufficiently high cosolvent concentrations, polymer-cosolvent interactions favor polymer unfolding.